Structural optimization of BeO (HCP structure) #1
Comments
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W dniu 27.06.2014 22:03, lim520 pisze:
I will try. But I need the notebook in the attachment (maybe in the zip Regards, Paweł T. Jochym |
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HI Dr.Jochym I have attached the notebook and the potentials used. With regards Linu On Fri, Jun 27, 2014 at 2:12 PM, Paweł T. Jochym [email protected]
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W dniu 27.06.2014 22:19, lim520 pisze:
I did not get any attachments. Try the zip file please. P. Paweł T. Jochym |
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HI Dr Jochym I have attached the zip file of notebook and potentials. With regards Linu On Fri, Jun 27, 2014 at 2:52 PM, Paweł T. Jochym [email protected]
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Hi Dr. Jochym
I was trying to do structural optimization of BeO with a space group of 186. But i was not able to optimize it to the same space group. Can you please go through the code i have used ( shown below) and guide me to know where i am committing mistake and what things should i do different.
{
"metadata": {
"name": "",
"signature": "sha256:1f946d3105d54e3c0582e10bc0200c4465e0d176d8bbc8d7352cc9625d0ae451"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Import the basic libraries\n",
"\n",
"# ASE system\n",
"import ase\n",
"from ase import Atom, Atoms\n",
"from ase import io\n",
"from ase.lattice.spacegroup import crystal\n",
"from ase.units import GPa, Bohr, Rydberg\n",
"\n",
"# Spacegroup/symmetry library\n",
"from pyspglib import spglib\n",
"\n",
"# iPython utility function\n",
"from IPython.core.display import Image\n",
"\n",
"# Import the remote execution tools from the qe-util package\n",
"from qeutil import RemoteQE\n",
"\n",
"import warnings\n",
"warnings.filterwarnings('ignore')\n",
"\n",
"# Access info\n",
"import hostp\n",
"\n",
"qe=RemoteQE(label='BeO-structure', # A name for the project\n",
" kpts=[3,3,3], # k-space grid\n",
" xc='pw91', # Exchange functional type in the name of the pseudopotentials\n",
" pp_type='van', # Variant of the pseudopotential\n",
" pp_format='UPF', # Format of the pseudopotential files\n",
" ecutwfc=70, # Energy cut-off\n",
" pseudo_dir='../pspot',\n",
" use_symmetry=False,\n",
" procs=16) # Use 8 cores for the calculation\n",
"\n",
"print qe.directory"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"calc/BeO-structure.f33j3k\n"
]
}
],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"a=2.7\n",
"c=4.4199\n",
"cryst= crystal(['Be', 'O'],\n",
" [(1/3., 2/3., 0), (2/3., 1/3., -1/8.)],\n",
" spacegroup=186,\n",
" cellpar=[a, a, c, 90, 90, 120])\n",
"# Assign the calculator to our system\n",
"cryst.set_calculator(qe)\n",
"\n",
"# Verify the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst)\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P6_3mc (186)\n"
]
}
],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress tensor (Voigt notation, GPa):\n", cryst.get_stress()/GPa\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress tensor (Voigt notation, GPa):\n",
"[-1.853 -1.853 2.58 -0. -0. -0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n"
]
}
],
"prompt_number": 3
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"cryst.rattle(stdev=0.05)\n",
"cryst.set_cell(diag(1+0.01_randn(3))_cryst.get_cell(), scale_atoms=True)"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Verify that indeed we have a low symmetry structure\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P1 (1)\n"
]
}
],
"prompt_number": 5
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Display the structure\n",
"ase.io.write('crystal.png', cryst, format='png', show_unit_cell=2, rotation='115y,25x', scale=30)\n",
"Image(filename='crystal.png')"
],
"language": "python",
"metadata": {},
"outputs": [
{
"metadata": {},
"output_type": "pyout",
"png": 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QdsQsWbJkyZLlIOf/g9iDbu/M2yUAAAAASUVORK5CYII=\n",
"prompt_number": 6,
"text": [
"<IPython.core.display.Image at 0xa7f9f0c>"
]
}
],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress tensor (Voigt notation, GPa):\n", cryst.get_stress()/GPa\n",
"\n",
"# Print also the forces (eV/A)\n",
"\n",
"print "\nForces on atoms (eV/A)"\n",
"print "======================"\n",
"print cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress tensor (Voigt notation, GPa):\n",
"[ -8.022 -84.177 -12.79 2.087 -0.245 49.47 ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces on atoms (eV/A)\n",
"======================\n",
"[[-0.00456724 0.00399573 0.0021234 ]\n",
" [ 0.00512782 -0.00498257 0.00401369]\n",
" [ 0.00560462 -0.00496495 -0.00302884]\n",
" [-0.0061652 0.00595179 -0.00310826]]\n"
]
}
],
"prompt_number": 7
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Switch to the atomic position relaxation mode\n",
"qe.set(calc='relax')\n",
"\n",
"# Switch off the use of symmetries. \n",
"qe.set(use_symmetry=False)\n",
"\n",
"# Force recalculation by clearing the results from the previous calculation.\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 8
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"\n",
"\n",
"# Run the calculation and get the stresses and forces at the end.\n",
"# The structure in cryst is not modified\n",
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 14.82 -78.361 38.072 -2.042 2.902 -0.593]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[-0.0003558 0.00047606 0.00075467]\n",
" [-0.00144971 0.00085408 -0.00112689]\n",
" [ 0.00055243 -0.00031167 -0.002229 ]\n",
" [ 0.00125308 -0.00101846 0.00260122]]\n"
]
}
],
"prompt_number": 9
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(forc_conv_thr=1e-8*Rydberg/Bohr)\n",
"qe.reset()\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 10
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"\n",
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 1.71940000e+01 -7.72210000e+01 4.11520000e+01 -0.00000000e+00\n",
" 1.10000000e-02 0.00000000e+00]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ 8.01212231e-07 2.37252165e-07 -8.82889205e-07]\n",
" [ 9.80123699e-08 -2.25584026e-07 -2.49892650e-06]\n",
" [ 1.32900106e-06 -2.01236509e-06 -2.43202916e-06]\n",
" [ -2.22822566e-06 2.00108589e-06 5.81345593e-06]]\n"
]
}
],
"prompt_number": 11
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the positions using calculated values\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry. Probably not the F-43m !\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P1 (1)\n"
]
}
],
"prompt_number": 12
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 13
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[-0.183 -0.304 -0.3 0.001 -0.002 0.002]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -1.50433430e-05 -1.17996003e-05 -1.90416254e-05]\n",
" [ 1.54653407e-05 1.14958398e-05 1.40694423e-05]\n",
" [ 1.89762838e-06 -7.93044533e-07 2.59032692e-06]\n",
" [ -2.31962609e-06 1.09680509e-06 2.38146723e-06]]\n"
]
}
],
"prompt_number": 14
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: Pm (6)\n"
]
}
],
"prompt_number": 15
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 16
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.048 0.052 0.06 0. -0.001 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -6.22300762e-07 -1.26793780e-07 -7.16034814e-07]\n",
" [ 3.67935325e-07 3.77269837e-07 2.17921948e-06]\n",
" [ 2.12749073e-07 -2.85480474e-07 -7.25758263e-07]\n",
" [ 4.16163634e-08 3.53933558e-08 -7.37815340e-07]]\n"
]
}
],
"prompt_number": 17
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P2_1 (4)\n"
]
}
],
"prompt_number": 18
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 19
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.195 0.197 0.199 0. -0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -4.46111858e-07 -1.12403075e-07 -2.17416329e-07]\n",
" [ 3.03760559e-07 2.69534017e-07 1.11858562e-06]\n",
" [ 1.51685811e-07 -2.11193321e-07 -4.56224246e-07]\n",
" [ -8.94557345e-09 5.36734407e-08 -4.44945045e-07]]\n"
]
}
],
"prompt_number": 20
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P2_1 (4)\n"
]
}
],
"prompt_number": 21
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 22
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.276 0.278 0.28 0. -0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -4.65169819e-07 -7.50650294e-08 -1.61798198e-07]\n",
" [ 3.07649939e-07 2.03025623e-07 9.29950701e-07]\n",
" [ 1.80856159e-07 -1.59075632e-07 -3.99050363e-07]\n",
" [ -2.29473406e-08 3.11150381e-08 -3.69102139e-07]]\n"
]
}
],
"prompt_number": 23
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P2_1 (4)\n"
]
}
],
"prompt_number": 24
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 25
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.011 0.011 0.014 0. 0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -1.87079166e-07 -8.40106028e-08 7.00088357e-08]\n",
" [ 1.52463687e-07 1.23682276e-07 1.77744655e-07]\n",
" [ 7.38982154e-08 -8.47884788e-08 -1.22126524e-07]\n",
" [ -3.96716736e-08 4.51168052e-08 -1.25626966e-07]]\n"
]
}
],
"prompt_number": 26
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: P2_1 (4)\n"
]
}
],
"prompt_number": 27
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 28
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.068 0.069 0.067 0. 0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -8.63442307e-08 -6.41747660e-08 3.96716736e-08]\n",
" [ 7.07867116e-08 7.23424635e-08 3.07261001e-08]\n",
" [ 4.58946812e-08 -3.65601697e-08 -3.65601697e-08]\n",
" [ -3.03371621e-08 2.83924722e-08 -3.38376039e-08]]\n"
]
}
],
"prompt_number": 29
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: C222_1 (20)\n"
]
}
],
"prompt_number": 30
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 31
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.438 0.438 0.433 0. -0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -6.10632622e-08 -4.04495495e-08 2.52809684e-08]\n",
" [ 7.97322851e-08 5.56181306e-08 -5.05619369e-09]\n",
" [ 2.02247748e-08 -1.82800849e-08 -1.28349532e-08]\n",
" [ -3.88937976e-08 3.11150381e-09 -7.77875952e-09]]\n"
]
}
],
"prompt_number": 32
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: C222_1 (20)\n"
]
}
],
"prompt_number": 33
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 34
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.394 0.394 0.387 0. 0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -5.25066268e-08 -4.23942394e-08 2.52809684e-08]\n",
" [ 4.74504331e-08 5.71738825e-08 -1.94468988e-09]\n",
" [ 3.30597280e-08 -2.02247748e-08 -1.43907051e-08]\n",
" [ -2.80035343e-08 5.05619369e-09 -8.55663547e-09]]\n"
]
}
],
"prompt_number": 35
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: C222_1 (20)\n"
]
}
],
"prompt_number": 36
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 37
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.396 0.396 0.389 0. 0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -5.25066268e-08 -4.20053014e-08 3.07261001e-08]\n",
" [ 4.74504331e-08 5.71738825e-08 -4.27831774e-09]\n",
" [ 3.30597280e-08 -2.02247748e-08 -1.59464570e-08]\n",
" [ -2.80035343e-08 5.05619369e-09 -1.05013254e-08]]\n"
]
}
],
"prompt_number": 38
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: C222_1 (20)\n"
]
}
],
"prompt_number": 39
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"qe.set(calc='vc-relax')\n",
"qe.reset()"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 40
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"print "Stress:\n", cryst.get_stress()/GPa\n",
"print "\nForces:\n", cryst.get_forces()"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Stress:\n",
"[ 0.141 0.141 0.137 0. -0. 0. ]"
]
},
{
"output_type": "stream",
"stream": "stdout",
"text": [
"\n",
"\n",
"Forces:\n",
"[[ -6.96198977e-08 -1.20570773e-08 1.24460152e-08]\n",
" [ 6.22300762e-08 2.45030925e-08 4.66725571e-09]\n",
" [ 6.02853863e-08 8.55663547e-09 -2.87814102e-08]\n",
" [ -5.28955647e-08 -2.10026507e-08 1.16681393e-08]]\n"
]
}
],
"prompt_number": 41
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"# Update the crystal\n",
"cryst.set_cell(qe.results['cell'])\n",
"cryst.set_scaled_positions(qe.results['atomic_positions'])\n",
"\n",
"# Check the symmetry\n",
"print "Symmetry group:", spglib.get_spacegroup(cryst,symprec=1e-4)"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Symmetry group: C222_1 (20)\n"
]
}
],
"prompt_number": 42
},
{
"cell_type": "code",
"collapsed": false,
"input": [
"\n",
"\n",
"# Round the sizes and positions to get to the high-symmetry structure\n",
"cryst.set_cell(np.round(qe.results['cell'],4))\n",
"cryst.set_scaled_positions(np.round(qe.results['atomic_positions'],3))\n",
"\n",
"# See the structure\n",
"print "Unit cell:\n", cryst.get_cell()\n",
"print "\nAtomic positions:\n", cryst.get_scaled_positions()\n",
"\n"
],
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": [
"Unit cell:\n",
"[[ 2.7155 -0. 0. ]\n",
" [-0. 2.7155 -0. ]\n",
" [-0. 0. 3.7903]]\n",
"\n",
"Atomic positions:\n",
"[[ 0.769 0.749 0.061]\n",
" [ 0.269 0.25 0.561]\n",
" [ 0.769 0.25 0.811]\n",
" [ 0.269 0.75 0.311]]\n"
]
}
],
"prompt_number": 43
},
{
"cell_type": "code",
"collapsed": false,
"input": [],
"language": "python",
"metadata": {},
"outputs": []
}
],
"metadata": {}
}
]
}
Regards
Linu
The text was updated successfully, but these errors were encountered: